Classes | |
class | breadth_iterator_t |
class | depth_iterator_t |
class | EndoplasmicReticulum |
class | GlialCell |
class | IDSequenceError |
class | MissingParentError |
class | Mitochondria |
class | MitoSection |
class | MorphioError |
class | Morphology |
class | MultipleTrees |
class | NotImplementedError |
class | RawDataError |
class | Section |
class | SectionBase |
class | SectionBuilderError |
class | Soma |
class | SomaError |
class | UnknownFileType |
class | upstream_iterator_t |
class | WriterError |
Typedefs | |
using | mito_upstream_iterator = upstream_iterator_t< MitoSection > |
using | mito_breadth_iterator = morphio::breadth_iterator_t< MitoSection, Mitochondria > |
using | mito_depth_iterator = morphio::depth_iterator_t< MitoSection, Mitochondria > |
using | breadth_iterator = breadth_iterator_t< Section, Morphology > |
using | depth_iterator = depth_iterator_t< Section, Morphology > |
using | upstream_iterator = upstream_iterator_t< Section > |
using | SectionRange = std::pair< size_t, size_t > |
using | MorphologyVersion = std::tuple< std::string, uint32_t, uint32_t > |
template<typename T > | |
using | range = gsl::span< T > |
using | floatType = float |
using | Point = std::array< morphio::floatType, 3 > |
using | Points = std::vector< Point > |
Enumerations | |
enum | SomaClasses { SOMA_CONTOUR, SOMA_CYLINDER } |
Functions | |
void | set_maximum_warnings (int n_warnings) |
void | set_ignored_warning (Warning warning, bool ignore=true) |
void | set_ignored_warning (const std::vector< Warning > &warning, bool ignore=true) |
void | printError (Warning warning, const std::string &msg) |
bool | diff (const Morphology &left, const Morphology &right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO) |
bool | diff (const Section &left, const Section &right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO) |
Point | operator+ (const Point &left, const Point &right) |
Point | operator- (const Point &left, const Point &right) |
Point | operator+= (Point &left, const Point &right) |
Point | operator-= (Point &left, const Point &right) |
Point | operator/= (Point &left, const floatType factor) |
Points | operator+ (const Points &points, const Point &right) |
Points | operator- (const Points &points, const Point &right) |
Points | operator+= (Points &points, const Point &right) |
Points | operator-= (Points &points, const Point &right) |
template<typename T > | |
Point | operator* (const Point &from, T factor) |
template<typename T > | |
Point | operator* (T factor, const Point &from) |
template<typename T > | |
Point | operator/ (const Point &from, T factor) |
template<typename T > | |
Point | centerOfGravity (const T &points) |
template<typename T > | |
floatType | maxDistanceToCenterOfGravity (const T &points) |
template Point | centerOfGravity (const Points &) |
template floatType | maxDistanceToCenterOfGravity (const Points &) |
std::string | dumpPoint (const Point &point) |
std::string | dumpPoints (const Points &point) |
char | my_tolower (char ch) |
floatType | distance (const Point &left, const Point &right) |
std::ostream & | operator<< (std::ostream &os, const morphio::Point &point) |
std::ostream & | operator<< (std::ostream &os, const Points &points) |
std::string | getVersionString () |
int | getMajor () |
int | getMinor () |
int | getPatch () |
Variables | |
constexpr floatType | epsilon = 1e-6f |
constexpr floatType | PI = static_cast<floatType>(M_PI) |
The property namespace is the core of MorphIO as it is where all the internal data are stored.
The higher level container structure is Property::Properties.
It contains low-lever structure that stores information at various levels:
Blue Brain File IO classes
using morphio::upstream_iterator = typedef upstream_iterator_t<Section> |
A class to represent a morphological section.
A Section is an unbranched piece of a morphological skeleton. This class provides functions to query information about the sample points that compose the section and functions to obtain the parent and children sections.
The cell soma is also considered a section, but some functions have special meaning for it.
Sections cannot be directly created, but are returned by several morphio::Morphology and morphio::Section methods.
This is a lightweight object with STL container style thread safety. It is also safe to use a section after the morphology from where it comes has been deallocated. The morphological data will be kept as long as there is a Section referring to it.
bool morphio::diff | ( | const Morphology & | left, |
const Morphology & | right, | ||
morphio::enums::LogLevel | verbose = morphio::enums::LogLevel::INFO |
||
) |
Perform a diff on 2 morphologies, returns True if items differ
bool morphio::diff | ( | const Section & | left, |
const Section & | right, | ||
morphio::enums::LogLevel | verbose = morphio::enums::LogLevel::INFO |
||
) |
Perform a diff on 2 sections, returns True if items differ
floatType morphio::distance | ( | const Point & | left, |
const Point & | right | ||
) |
Euclidian distance between two points
void morphio::set_maximum_warnings | ( | int | n_warnings | ) |
Set the maximum number of warnings to be printed on screen